In my case I didn't get that much variability. But since our fluctuations in the configuration were only there immediately after the upgrade, it is perhaps because easy-deb-chroot did overwrite some of the configuration files of LXDE. One file that is for sure overwritten by an upgrade is the one for the top panel, because I had to change that back to what I had before. Did you do some more extensive modifications of the layout, mscion?

qole, I think it would be best if an upgrade of easy-deb-chroot would generally leave /home/user/.config files as they are, when they are already there, and instead install them with -dist appended or something. If easy-deb-chroot is installed freshly, it's of course desirable to have a consistent complete set of those config files installed (even if some were left over after de-installing easy-deb-chroot).